External Email - Use Caution
Yes! And please do use the latest version
Sent from my phone, please excuse brevity and typos
From: Sally Grace Sent: Thursday, June 14, 05:49 Subject: Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3? To: Freesurfer support list
External Email - Use Caution Hi Eugenio,
Great. We have already run our subjects through recon-all for FS5.3. EG. recon-all -s [subjects_dir]
We have two dev versions of freesurfer installed on our server: freesurfer/devel-20180612 and freesurfer/devel-20171013. Does it make any difference if we use either version? We aim to use freesurfer/devel-20180612 as it is the latest.
We have T1 crossectional data processed using FSV5.3 recon-all. Can I bypass running recon-all again and directly perform the segmentation via the command below (without typing in recon-all at the start of the terminal?):
segmentHA_T1.sh [SUBJECTS_DIR]
Kind regards, Sally.
Sally Grace BSc (Hons), PhD Candidate. Centre for Mental Health Faculty of Health, Arts and Design | Swinburne University of Technology Hawthorn, 3122
(03) 9214 8415
sallyagracemailto:sallyagrace@gmail.com@gmail.commailto:sallyagrace@gmail.com (preferred) | sgracemailto:sgrace@swin.edu.au@swin.edu.aumailto:sgrace@swin.edu.au
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Sent: Wednesday, 6 June 2018 6:09:24 PM To: Freesurfer support list Subject: Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?
External Email - Use Caution Dear Sally, You will need to download the development version to access this functionality. However, if you have already run your subjects through recon-all with FS5.3, you can directly call segmentHA_T1.sh/ segmentHA_T2.sh/ segmentHA_T1_long.sh in the dev version (no need to run recon-all again with dev). Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London httphttp://www.jeiglesias.com://www.jeiglesias.comhttp://www.jeiglesias.com httphttp://cmictig.cs.ucl.ac.uk/://cmictig.cs.ucl.ac.uk/http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sally Grace sgrace@swin.edu.au Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 6 June 2018 at 03:16 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?
External Email - Use Caution Hi there,
I wish to segment amygdala nuclei in Freesurfer Version 5.3, is it possible? I can find documentation only for Freesurfer version 6.0 here (httpshttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala://surfer.nmr.mgh.harvard.edu/https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdalafswikihttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala/https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdalaHippocampalSubfieldsAndNucleiOfAmygdalahttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala). Can the scripts be adapted to Freesurfer v5.3?
Thanks in advance, Sally. https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala HippocampalSubfieldsAndNucleiOfAmygdala https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala - https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Free https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Surfer https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Wiki
http://surfer.nmr.mgh.harvard.edu surfer.nmr.mgh.harvard.edu
Segmentation of hippocampal subfields and nuclei of the amygdala ( cross - sectional and longitudinal) This functionality has been available in the development version of FreeSurfer since August 31st 2017